2012 iGEM

CBNU-Korea

July

July. 2nd – July. 5th

Monday

■A : Found the searching method of the Bio-brick to run a software, and reviewed how to design the software.

■B : Made the chart of 4 species.
(Used same algorithm as the previously used). 4 species list : Escherichia_coli_str_K-12_substr_MG1655, Pseudomonas_aeruginosa_UCBPP-PA14, Salmonella_enterica_substr_enterica_serovar_Typhimurium_str_LT2, Heamphilus_influenzae_Rd_KW20

■C : Set standard based on genes which is existing in the every species.

Tuesday

■A : Made questionnaire to be held with instructors.

Thursday

■A : Reviewed the questionnaire. Discussed about additional GUI form.

■C : Set standard of division on genome.

July. 5th – July. 10th

Thursday

■B : Expanded the process to every 17 species. Annotated Synb_Code to each genes & Drew a chart.
(The genes contained in every 17 species : 48 List of 17 species : (http://cafe.naver.com/synb2011/314)
Blast standards : identity > 25%, |Length| < 5%, e-value > 0.05, bit-score > 200.

July. 9th – July. 15th

Monday

■A : Studied codon optimization.

Wednesday

■A : Studied Promoter profiling.

■B : Got some of opinions about setting standard of BLAST from instructors. Found a new standard through other processes.
Blast standards
Standard 1 : identity > 25%, |Length| < 15%, e-value : None, bit-score : None.
Standard 2 : identity > 25%, |Length| < 15%, e-value: < 0.05, bit-score < 50.
Standard 3 : identity > 25%, |Length| < 15%, e-value < 0.05, bit-score : None.

Thursday

■A : Discussed to implement SBOL or not.

■B : Studied UID theory to annotate SynB UID.

■C : Compared the strand of genome & Analyzed strand pattern.

Friday

■C : Began to analyze with the result of Standard 1 and standard 2.

Saturday

■A : Studied SBOLC Library to implement the function of saving as SBOL format .

■B : Studied what gene to use as a standard and what kind of analysis should we use.

July. 16th - July 22th

Monday

■A : Summarized research papers. Exchanged information with other universities(Ulsan National Institute of Science and Technology, Korea University)

■B : It taked too much time to analyze. Set SynB UID concept, approximately.

■C : Simulated on analysis of strand pattern. Studied how to use analysis on strand(+/-).

Tuesday

■A : Worked on document & Tried to find sponsors.

■B : Started to specify requirements of SW to begin implementing SW.

Wednesday - Thursday

■B : Developed new analysis algorithm. It only takes 30 minutes to analyze which took a week before.

Thursday

■A : Discussed about the method of design to adjust requirements into SW well.

■B : Implemented SAS program to calculate confidence interval(statistic word) by sorting genes based on newly annotated Synb UID.

Friday

■A : Started to design DB table to use in SW.

■B : Approximate Organized the requirements of SW through consultation with the instructors.

■C : Drew a Graphed of strand(+/-) pattern of each gene in genome.

Saturday

■B : Due to a power outage, had to run the analysis program again. However because of this we could improve the algorithm.

July. 23rd – July. 29th

Monday

■A : Started to study GDI+ to implement graphic part of SW.

■B : Organized primary requirements of SW.

■C : Summarized research paper. (?compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-sprecific gene and conserved structural features and sequence motifs)

Tuesday

■B : Organized requirement document with additional requirements.

July. 25th - July. 26th

Thursday

■A : Produced Bio-Brick icon of each type which are going to be used in SW.

■B : Implemented new annotation algorithm. Ran program with it.

■C : Considered method of analyzing strand, Based on research papers.

Friday

■B : Identified annotation.

■C : Divided genome into 100 section to analyze strand pattern. Calculated strand percentage.

July. 30th – July. 31st

Monday

■A : Implemented function of image shifting for Bio-Brick synthetic.

■B : Set targets of Blast analysis, Bacteria Gamma. Modified existing algorithm of analysis. Started to analyze by using all of the computers in lab.
Blast standard 1 : identity > 25%, |Length| < 5%, e-value > 0.05, bit-score > 200.
Blast standard 2 : identity > 30%, |Length| < 5%, e-value > 0.05, bit-score > 200.
Blast standard 3 : identity > 30%, |Length| < 15%, e-value > 0.05, bit-score > 50.

■C : Analyzed strand using statistical program of SAS and R.

Tuesday

■A : Implemented interval function of Bio-Brick synthetic.

■B : Result of Blast wasn’t good enough. Set standard of Blast differently.
Blast standard 1 : identity > 20%, |Length| < 15%, e-value < 0.05, bit-score > 200
Blast standard 2 : identity > 30% |Length| < 5%, e-value < 0.05, bit-score > Query Length / 3

■C : Analyze on calculating confidence interval(statistic word) had been failed.